mmg_233_2013_genetics_genomicswikiaorg-20200214-history
Evolution of Human Coronavirus
Coronavirus Introduction This virus was first recorded in the 1960s when it was found in the nasal cavities of patients with the common cold. It belongs to one of two subfamilies Coronavirinae ''and ''Torovirinae ''in the family ''Coronaviridae ''(Coronavirus, 2013). The name coronavirus comes from the latin term "corona" meaning crown which correlates with the crown-like spikes on their surface. The three main sub-groupings of this virus are alpha, beta and gamma and the five viruses that can infect people are alpha viruses 229E and NL63 and beta viruses OC43, HKU1 and SARS-CoV. SARS is the well known virus that causes acute respiratory distress and was a huge source of fear in the early 2000's (About, 2013). Coronaviruses have a positive-sense RNA genome and a nucleocapsid of helical symmetry and they exhibit a genome that is extraordinary large for a virus(Coronavirus, 2013). They are also unique in the virus world because they have a high frequency of RNA combination as a result of random template switching during RNA replication. This paired with a high mutation rate allows for quick adaptation in new hosts and niches. These viruses are known for their ability to cause infections in a large variety of animals which results in hepatic, enteric, respiratory and neurological diseases of varying levels of severity (Molecular, 2010). Study Methodology Twenty-nine HCoV-OC43 strains of coronavirus were detected in patients who had been admitted to Queen Mary Hospital and Pamela Youde Nethersole Eastern Hospital in Hong Kong. The patients came in exhibiting acute respiratory infections, and all 29 patients were selected over a seven-year period. Participants tested negatively for influenza, parainfluenza, respiratory syncytial virus, adenovirus, HKU1, human coronavirus 229E and NL63. Viral RNA was extracted from patients using a QIAamp viral RNA Minikit and the RNA pellet was eluted in DNase-free, RNase-free water. This RNA was used as a template for RT-PCR sequencing of the complete RDRP, S and N genes, and the genes were then amplified. The RNA was then converted to cDNA and finally the RDRP, S and N genes were compared to HCoV-OC43. A maximum-likelihood methodology was used to form a phylogenetic tree for the genes present and the branches were assessed by bootstrap analysis. Two complete genomes of the HCoV-OC43 strain of the coronavirus were completely sequenced and the 5’ ends of the viral genomes were confirmed by the rapid amplification of cDNA ends. The nucleotide and amino acid sequences of the genomes were compared to the other coronaviruses using CoVDB and another phylogenic tree was formed using the neighbor-joining method. The number of synonymous substitutions, Ks, and the number of nonsynonymous substitutions, Ka, for each coding region was calculated using the Nei and Gojobori substitution model. Divergence was estimated using a Bayesian Markov chain Monte Carlo. The trees were summarized in a target tree by the BEAST package by choosing the tree with the maximum sum of posterior probabilities (Molecular). Results Analysis showed three clusters of HCoV-043 that suggested the presence of four HCoV-OV43 genotypes (A through D). They theorized that genotype D had most likely arisen from recombination. The complete genome analysis done on strands C and D showed a crossover between B and C that was represented in genotype D. Though none of the 29 strands belonged to the oldest genotype A, 5 from 2004 belonged to genotype B, 15 from 2004 to 2006 belonged to genotype C, and 1 from 2004 and all 8 from 2008 to 2011 belonged to the recombinant genotype D. Further analysis using molecular clock technology and nucleocapsid genes found that a common ancestor for all the genes was likely present in the 1950s, a common ancestor for B and C was present in the 1980s. Genotype B was said to have diverged in the 1990s, C diverged in the late 1990s to early 2000s and the recombinant form of D arose in 2004. This is the first study of its type done on coronavirus HCoV-0V43 (Molecular). Works Cited "About Coronavirus ." Centers for Disease Control and Prevention, 12 Mar. 2013. Web. 12 Dec. 2013. . Coronavirus . (2013, December 6). In ''Wikipedia, The Free Encyclopedia. Retrieved 23:01, December 12, 2013, 'Molecular Epidemiology of Human Coronavirus OC43 Reveals Evolution of Different Genotypes over Time and Recent Emergence of a Novel Genotype due to Natural Recombination , '